Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.

References:

• Roth et al. PyClone: statistical inference of clonal population structure in cancer PMID: 24633410

• https://github.com/aroth85/pyclone

• Module Name: pyclone (see the modules page for more information)
• Example files in /usr/local/apps/pyclone/examples

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pyclone
[user@cn3144 ~]$ cp -r /usr/local/apps/pyclone/examples /data/$USER
[user@cn3144 ~]$ cd /data/$USER/examples/mixing/tsv
[user@cn3144 ~]$ PyClone run_analysis_pipeline --in_files SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir pyclone_analysis
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

This will create a directory pyclone_analysis. After the command completes the directory will contain several folders and the file config.yaml:

• config.yaml
• plots/
• tables/
• trace/
• yaml/

The contents of these folders are as follows:

• config.yaml - This file specifies the configuration used for the PyClone analysis.
• plots - Contains all plots from the analysis. There will be two sub-folders clusters/ and loci/ for cluster and locus specific plots respectively.
• tables - This contains the output tables with summarized results for the analysis. There will be two tables clusters.tsv and loci.tsv, for cluster and locus specific information.
• trace - This the raw trace from the MCMC sampling algorithm. Advanced users may wish to work with these files directly for generating plots and summary statistics.

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load pyclone
PyClone run_analysis_pipeline --in_files SRR385939.tsv SRR385940.tsv SRR385941.tsv --working_dir pyclone_analysis

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1;PyClone ...
cd dir2;PyClone ...
cd dir3;PyClone ...
cd dir4;PyClone ...

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module pyclone

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module	Loads the module for each subjob in the swarm